Jude the Obscure is an account of the doomed existence of the protagonist named in the title, from the moment he is first inspired by a rural schoolmaster to think of a university education as the highest possible attainment, to his dying alone, while hearing celebratory shouts and organ notes in the distance from Remembrance Day at Christminster University, a place which has given not the slightest heed to his ambitions. Between these two moments are twenty years of self-directed study, and defeats in sex and love inflicted on him by two women, one sensual and pragmatic, the other intellectual and intensely seeking.

The intellectual woman, Sue Bridehead, is Jude's cousin. In effect she is the novel's co-protagonist although not named in the title; she is arguably Hardy's most challenging character to understand. Jude's mother and Sue's father were siblings, and had experienced disastrous marriages, the basis for one of the novel's minor themes, that some people are poor candidates for marriage. On top of what is taken to be a family curse is the reprehensible and constricting nature of marriage itself as Jude and Sue perceive it. The times and their own personalities conspire to thwart their best intentions and hopes. Well-meaning, intermittently sensitive to the other’s needs while usually insistent upon the inherent justice of his and her own needs, the couple interact with a rawness of ego that includes lacerating self-condemnation. The novel’s characterizing tone is bitterness, seemingly unmediated because the narrator shares the characters' sense of outrage that society censures both their unconventional sexual relations and their idealism.